JAL-2556 start to account for wrapped alignments

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index e999e78..558c1ca 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -936,8 +936,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
               if (sx < 0)
               {
-                // ex += sx;
-                // sx = 0;
+                ex += sx;
+                sx = 0;
               }
 
               if (sx + ex > visWidth)
@@ -1034,6 +1034,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    */
   private BufferedImage drawSelectionGroup()
   {
+    int verticalOffset = 0;
+    if (av.getWrapAlignment())
+    {
+      verticalOffset = charHeight;
+      if (av.getScaleAboveWrapped())
+      {
+        verticalOffset += charHeight;
+      }
+    }
+
     // get a new image of the correct size
     BufferedImage selectionImage = setupImage();
 
@@ -1051,6 +1061,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     // set up drawing colour
     Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+    g.translate(LABEL_WEST, 0);
     // set background to transparent
     g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
     g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
@@ -1079,7 +1090,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int startSeq = av.getRanges().getStartSeq();
     for (i = startSeq; i <= av.getRanges().getEndSeq(); ++i)
     {
-      int sy = (i - startSeq) * charHeight;
+      int sy = verticalOffset + (i - startSeq) * charHeight;
 
       if (group.getSequences(null)
               .contains(av.getAlignment().getSequenceAt(i)))
@@ -1145,7 +1156,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     }
     if (inGroup)
     {
-      int sy = (i - startSeq) * charHeight;
+      int sy = verticalOffset + (i - startSeq) * charHeight;
       if (startx >= 0 && startx < visWidth)
       {
         g.drawLine(startx, oldY, startx, sy);
@@ -1175,7 +1186,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       inGroup = false;
     }
-
+    g.translate(-LABEL_WEST, 0);
     return selectionImage;
   }